Variant report

Variant	rs11862593
Chromosome Location	chr16:79824781-79824782
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10871380	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11150199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11150200	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11150201	0.97[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11150202	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11150203	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11150204	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11150205	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11150206	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11150207	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11150208	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11150209	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11150210	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11150211	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11150212	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11150213	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11150214	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11150215	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11150216	0.97[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11150219	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11150220	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1134715	0.97[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11640405	0.90[ASN][1000 genomes]
rs11640419	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11642817	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11643810	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11648556	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11648855	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11860693	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11862561	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11863874	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11866244	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12444097	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12444100	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12444123	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12446125	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595956	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12597506	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12598926	0.94[CHB][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12600157	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12919529	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12920397	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12923698	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12925344	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12928764	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12930441	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12931444	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12931584	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12934885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13336602	0.90[AFR][1000 genomes]
rs3935177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4243183	0.81[TSI][hapmap]
rs4243184	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4299168	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4392086	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4538028	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4584830	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4611477	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4636922	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4888047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4888048	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4888049	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4889028	0.81[AFR][1000 genomes]
rs4889029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889032	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4889033	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4889034	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4889035	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6564706	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7187906	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7191989	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8043824	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs8059641	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9939031	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11862593	SDR42E1	cis	cerebellum	SCAN
rs11862593	GAN	cis	cerebellum	SCAN
rs11862593	CHST6	cis	cerebellum	SCAN
rs11862593	CHST5	cis	parietal	SCAN
rs11862593	RP11-345M22.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79814000-79839600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:79823400-79827800	Weak transcription	NHEK	skin
3	chr16:79823600-79829000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr16:79823600-79829800	Weak transcription	Esophagus	oesophagus
5	chr16:79824200-79826600	Enhancers	Ovary	ovary
6	chr16:79824200-79829400	Enhancers	Fetal Stomach	stomach
7	chr16:79824400-79824800	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr16:79824600-79824800	Enhancers	Duodenum Mucosa	Duodenum
9	chr16:79824600-79826600	Enhancers	Fetal Lung	lung

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